6FNN

Caldiarchaeum Subterraneum Ubiquitin:Rpn11-homolog complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system.

Fuchs, A.C.D.Maldoner, L.Wojtynek, M.Hartmann, M.D.Martin, J.

(2018) Nat Commun 9: 2696-2696

  • DOI: 10.1038/s41467-018-05198-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archa ...

    While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archaeal Rpn11 deubiquitinase from Caldiarchaeum subterraneum, CsRpn11, and its role in the processing of CsUb precursor and ubiquitinated proteins. CsRpn11 activity is affected by the catalytic metal ion type, small molecule inhibitors, sequence characteristics at the cleavage site, and the folding state of CsUb-conjugated proteins. Comparison of CsRpn11 and CsRpn11-CsUb crystal structures reveals a crucial conformational switch in the CsRpn11 Ins-1 site, which positions CsUb for catalysis. The presence of this transition in a primordial soluble Rpn11 thus predates the evolution of eukaryotic Rpn11 immobilized in the proteasomal lid. Complementing phylogenetic studies, which designate CsRpn11 and CsUb as close homologs of the respective eukaryotic proteins, our results provide experimental support for an archaeal origin of protein ubiquitination.


    Organizational Affiliation

    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany. joerg.martin@tuebingen.mpg.de.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit N11-like protein
A, B
155Caldiarchaeum subterraneumMutation(s): 0 
Find proteins for E6N8B9 (Caldiarchaeum subterraneum)
Go to UniProtKB:  E6N8B9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein
C, D
104Caldiarchaeum subterraneumMutation(s): 0 
Find proteins for E6N8B8 (Caldiarchaeum subterraneum)
Go to UniProtKB:  E6N8B8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.674α = 90.00
b = 94.571β = 90.00
c = 170.855γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-07-25
    Type: Initial release